Half Life: Alternating Timelines
by Anubis424242
Summary: While Gordon Freeman is fighting with the rebels in City 17, the enemy and its technology begins to disappear and no one but the Gman knows why. It seems that a new race of aliens no one has met before desired to have the power of the Combine empire and decide to change history and take that power from the Combine.
1. Disappearances

Deep within City 17, the battle between the rebels and the Overwatch troops raged. Striders marched through the streets, shooting down any rebels they came across and destroying structures that stood in their way with their warp cannons. Suffering from heavy casualties, the rebels began loosing morale. They continued to fight, in spite of the fear that their efforts were pointless, preferring to die fighting, over being captured and taken into the Citadel to be implanted with Combine technology.

Luckily, when all hope seemed to be lost, Gordon Freeman joined the battle. His HEV suit protected him from his enemies, including the bullets of the pulse cannons on the striders, as long as he kept it fully charged. Every rebel that greeted him received a nod in response and nothing more. Gordon was a silent fellow and kept his thoughts to himself.

From distant locations, a mysterious man with the ability to control time and teleportation observed Gordon. As Gordon Freeman fought against striders just outside of the Overwatch Nexus, the mysterious man adjusted his tie and watched, invisible to everyone involved in the fight.

Gordon Freeman found a cache of RPG rounds and began to load up the RPG he had been carrying with him from the roof of the Overwatch Nexus, so he could begin firing at the striders. He aimed at the first one he saw and fired. However, before Gordon could hit his target, the strider simply vanished. Gordon's face was overcome with an expression of surprise. Even the rebels in the area noticed and they could not believe their eyes.

"What the hell?!" many cried. Some even wondered if this was a miracle. "Could a god be responsible for this?"

Beyond the Overwatch Nexus, Gordon watched as the Combine Citadel vanished. The mysterious man that had been watching Gordon ever since Black Mesa, also noticed what was happening. He became frustrated because he knew the cause of the disappearances and did not like it. This was not part of his plan. He immediately teleported Gordon from the scene and put him in stasis again, while Combine technology continued to disappear.


	2. The Queen

Smoke rose up from the ruins and all of the dead bodies as the ships fired down upon the Combine home world. They had traveled back in time 100,000 years and entered the dimension of the Combine to eliminate them. The commander of the fleet was the queen of a species of creatures that all had scaly, green skin, beaks for mouths, and had four legs for traveling, though they were able to travel on two legs as well, which was necessary when using their energy-based rifles. This species was also able to use all four of their feet as hands, each with three fingers and two opposable thumbs.

When the resonance cascade first occurred on the Earth, this species knew what had happened, even though their area of space was unaffected. The Earth was located in one of the sectors occupied by this species, though the Earth itself was never under their control. Upon the Combine's occupation of the Earth, they had been observing in cloaked ships, even running scans on the Combine technology. Their scanning technology was extremely advanced and the Combine never detected the scans.

Nonetheless, Combine technology was far more advanced than that of this species in more ways than one. Using schematics attained from the scans, they returned to their main sector and began to build prototype vessels that would be integrated with Combine technology. Every member of the queen's empire was jealous and greedy and coveted the power the Combine had. Once their ships had been integrated with Combine technology, the new prototype ship was tested to see if it could enter Combine space while cloaked. The test was successful.

The queen had her species build a fleet of ships, all integrated with Combine technology. However, knowing that a war with the Combine would result in heavy casualties on both sides, the queen devised a plan to build a transporter that would allow the queen to send her ships back in time to eliminate the Combine while they were at a primitive stage in their development. If they were to eliminate the Combine at their home world before they could advance, the Combine would never rise to power and the queen would have everything she wanted.

The project to build the time transporter was a long and difficult project. During the project, the queen's scientists learned more about Combine technology and discovered better ways to merge Combine technology with theirs. Their improved methods made the project a success.

When the project was complete, the transporter was placed in orbit around a small, uninhabited planet in their main sector. The transporter resembled a large, metallic square that was large enough to fly warships and even the queen's mother ship through. At the center was a giant green teleport that would send any ship back in time 100,000 years.

When the ships went through the transporter, they went back in time 100,000 years to that same area of space. Then, using special engines, the ships created windows into the Combine's dimension and the entire fleet entered Combine space. In only a matter of moments, the queen's fleet found the Combine home world and prepared to begin their attack.

The Combine advisors on the planet detected the ships immediately. The Combine, however, were not as advanced as their attackers because they were at a fairly early and primitive stage in the development of their species and technology. From the surface of the planet, explosive torpedoes were fired up into the air at the attacking ships. They were harmlessly reflected by the protective force fields around the ships and then the ships began to fire upon the planet.

The smell of burning flesh filled the air as the Combine advisors and other species native to their world, that they had enslaved, were killed in the massive explosions created by the attacking ships.

From aboard the mother ship, the queen watched the explosions on her view screen. She watched as the massive explosions on the planet's surface sent massive clouds of dust into the air and left giant craters in the ground. The queen hissed quietly and said to the team that was controlling her ship from the bridge, "We have succeeded. Their power now belongs to us. Send a signal to all of the other ships telling them that it is time to enter our space once again. When we return, I want the transporter to be destroyed."

The queen's fleet returned to normal space and destroyed the time transporter. Then, the queen commanded her fleet to return to their home world to begin building their civilization. With 100,000 years available to advance, the queen's species would be able to build an empire that would be several times more powerful than their empire had been in the original timeline.


	3. The Freeman

At Black Mesa, a project to build a space ship that could leave the solar system, equipped with a special engine that would allow the ship to fly faster than the speed of light, through subspace, had finally been completed. It was the year 2020 and the project had been underway for seven years before completion. The project had been shut down once before, twenty years earlier, before it was resumed on November 27, 2013.

It was time for the very first test-flight. Dr. Gordon Freeman entered the bridge, with his HEV suit on. He was ready to begin the test-flight. Like many members of the crew, Gordon was disappointed that Aperture had completed their first space craft, equipped with an FTL engine, two years before Black Mesa's was completed.

When Gordon got to the bridge, he said, "Alright, we are ready to go!" Dr. Isaac Kleiner, who had white hair all over the top of his head and a small white mustache above his upper lip, Dr. Eli Vance, and Dr. Arne Magnusson, along with a small crew from the U.S. Air Force, powered up the ship's main engine, so they could fly up and leave the Earth's atmosphere. "Begin lift off on my mark," Dr. Kleiner said. He counted down from ten and then the ship left the ground. Dr. Magnusson, who was the leader of the project, held up both of his hands and shouted out in excitement, "Lift off!" and then laughed. "If it had not been for me, then Black Mesa's administrator would never have permitted us to resume the project!"

Gordon approached Dr. Magnusson. "Hey, don't I deserve some of the credit? Had it not been for my expertise in theoretical physics, we would never have been able to put these systems together from the schematics and materials given to us by our sponsor back in 2000."

Dr. Magnusson stepped back. "I am sorry Doctor Freeman. I realize that without you, this project may never have succeeded. I can not begin to imagine how Aperture could have completed their ship without you!"

"I was thinking, instead of calling this ship by its project number, how about we name it after me!" Gordon said excitedly. Dr. Kleiner pointed up into the air excitedly. "Excellent idea Gordon! We should name it 'The Freeman'!"

The navigation crew steered the ship towards the sky and flew up into the Earth's atmosphere. Dr. Vance contacted Black Mesa's administrator so she would know that the ship had left the surface.

"Excellent work Doctor Vance," said the administrator. "Your team has done a fine job on this project in the past seven years."

"Well Doctor Mossman, even though the project was resumed seven years ago, we made most of our progress in the past four years, after Doctor Freeman returned to us."

On the screen in front of Eli, Dr. Judith Mossman, who replaced Dr. Wallace Breen as the administrator in 2018 when Dr. Breen left Black Mesa, smiled. "Well, he is a fine scientist. Even though I also applied for his position in Sector C when the FTL project first started, Doctor Freeman was more deserving of the job than I was. He will make a fine administrator for the engineering team on the ship. Good luck on the test-flight."

The connection between Black Mesa's administrative office and the Freeman was severed. About three minutes later, the Freeman left Earth's atmosphere and entered space. Dr. Magnusson looked at Gordon. "Well Mister Freeman, you better return to your station at FTL Management."

Gordon nodded. "Yes sir." Gordon left the bridge and hurried to join the engineering team, so they could activate all of the different systems required to activate the FTL engine. Along the way, Alyx Vance, Eli's daughter, happened to see Gordon as he was passing through the maintenance corridor she happened to be working in. She watched him hurry away and then returned her focus to the work she was doing. She was extremely attracted to Gordon, but was too shy to try and confront him about her feelings. Ever since she had been given the opportunity to work as an intern for her own father, she had enjoyed working on the FTL project, but Gordon had always been a distraction for her and she felt nervous when he was around.

When Gordon arrived at FTL Management, he and his crew got to work in preparing all of the systems required to turn on the power for the FTL. The FTL engine was a five foot tall cylinder with a circumference of eight feet, with several small consoles attached to it. Gordon activated the containment field around the power core, because it was required to prevent the core from becoming unstable. The instability of the energy source inside of the core had been the cause of a very serious incident in Sector C of Black Mesa in the year 2000, where the FTL project first began before it was temporarily shut down.

"Alright everyone, let's get this party started!" Gordon shouted. Everyone was at an assigned console and Gordon gave everyone instructions. Once everything was ready, Gordon gave the navigation team the signal that the engine was ready through the intercom system. "Freeman to Bridge, plot your coordinates and then we will open up the subspace window."

The navigation team plotted their coordinates and then Gordon activated the hyperspace systems in the FTL engine and the ship entered subspace. The ship was now on its way to the chosen coordinates, which were the coordinates of a planet that had been discovered by NASA two months earlier, to see if life existed on that planet.


	4. Prepare for Unforeseen Consequences

Gordon remained in the Systems Control Sector on deck three to make sure that all of the systems on the Freeman were operating efficiently. Gordon also checked to make sure that the ship's protective force field, which had also been created with materials and instructions, provided by the mysterious sponsor back in 2000, was online. The system was working properly. However, the shield could not be active when the ship was in subspace.

As the leader of the engineering team, it was Gordon's job to pay close attention to everything for the test-flight. During his inspections, Alyx Vance entered the Systems Control Sector to speak with Gordon. She eventually found him in Safety Management, while he was hoping to discover a way to activate the protective force field while in subspace, just in case the Freeman happened to enter into space controlled by unfriendly aliens that humans had never encountered before.

"Um, Mister Freeman." Gordon heard Alyx's voice behind him and he turned around to face her. "Hello Miss Vance."

"Is there anything I can do to help?" Alyx asked. Gordon shook his head. "My team already has everything under control. However, I can show you how many of the systems in this sector work, so that maybe one day you can be a part of the engineering team."

Alyx smiled. "I would like that." Then her smile quickly faded. Gordon raised an eyebrow. "Miss Vance, why do you seem nervous?" Alyx shook her head. "I'm not nervous. I'm just a little bit excited about meeting you and maybe learning about managing the systems on this ship."

Gordon pulled off his glasses and smiled flirtatiously at Alyx, who he thought was a very attractive young woman. "You are excited about meeting… me?"

"Well, you're a very famous guy around here," Alyx said quietly. "Ever since you returned to Black Mesa after the accident you were involved in, everyone has always talked about you. I don't know anything about the accident, but I know that it was serious and that you stopped working at Black Mesa for many years."

"You're right, it was serious," Gordon said as his smile faded. "I have no memory of anything between the accident and when I rejoined this project. For some strange reason, I also never aged in all that time. I still look as young as I did twenty years ago."

Their conversation was suddenly interrupted when there was a rumble nearby and an alarm began to go off. "Miss Vance, return to your quarters immediately!" Gordon instructed. He hurried to FTL Management and that is when he realized that the core was becoming unstable and was about to go critical. The containment field was still in place and Gordon hoped it would prevent another incident like the one at Black Mesa twenty years earlier.

In spite of what Gordon had said, Alyx did not return to her quarters. She went into FTL Management to watch what was happening. She watched as Gordon opened up the access to the core, so he could see what was happening inside. Inside of the core, the energy ball contained in the dark matter bounced around inside of the containment field.

Systems all around the FTL engine began to short circuit and sparks flew out of some of the consoles. "Shut it down!" Gordon screamed. "Shut the damn thing down!" The Freeman began to shake from the explosions that occurred within the FTL engine. Dr. Magnusson contacted Gordon through the intercom system. "Mister Freeman, what the hell is happening over there?"

"The FTL core is destabilizing and the systems are beginning to short circuit! We're attempting to shut down the system! As long as the containment field is still in place, we should be able to avoid destroying the engine!"

"Get those systems shut down Freeman! I don't want to see another disaster like in Black Mesa!" Dr. Magnusson terminated the intercom link while Gordon resumed shutting down the FTL engine. The power controls on the console were not responding, so he had to try a manual shut down, by unplugging the engine from the ship's main power source. He hurried to the power panel and unplugged the systems to cut off the supply of power to the engine.

As soon as Gordon did this, the Freeman entered normal space again. Alyx hurried over to Gordon. "What happened?!" Gordon suddenly became angry. "I thought I told you to go back to your quarters! Get the fuck out of here now damn it!" Alyx did as she was told and ran back to her quarters. However, she had been frightened by Gordon's anger and had not expected him to scream at her like that. She sat down on her bed and cried.

Meanwhile, back in FTL Management, the repair team hurried into the control room and got to work repairing the FTL engine. Gordon remained to give the team instructions for interacting with the FTL engine systems. When he was sure the repair team could manage without him, he decided that he needed to apologize to Alyx for his behavior. He knew he had hurt her when he watched her run away from him.

He went to Deck four, Sector D, where he could find Alyx's quarters. He knocked on her door and asked her if he could come in. Her voice was shaky, when she told him he could enter. Gordon pushed the button on the wall outside of the door and then the door opened.

"I've come to apologize for my behavior Alyx," Gordon said. He sat down on Alyx's bed next to her. "I was just so freaked out about what happened that I was unable to control myself. I hope you can forgive me."

Alyx wiped the tears off her face and nodded. "I can forgive you. I know that the situation was bad and that I was not supposed to be there, but I was just frightened by your reaction."

Just then, Dr. Eli Vance entered the room. "Alyx!" Alyx jumped up and hugged Eli. "Dad!" she shouted. "Hello Gordon," Eli said when he noticed Gordon there. Alyx returned to her bed and then Eli folded his arms. "So, what are the two of you discussing in here?"

Gordon stood up. "I was apologizing to her for my behavior, Eli. I yelled at her when the FTL engine began to malfunction and I had to see if she was okay."

Eli unfolded his arms and he became worried. "Why were you in FTL Management Alyx?" Alyx didn't reply. She just stared at the floor. Gordon stood up and tried to explain. "Sir, I think she was curious to see what was happening even though I told her to leave when the systems began to malfunction. When I realized she was still there after I shut off the power to the FTL engine, I screamed at her and told her to leave."

"I can understand your reaction," Eli said. "Alyx, when systems begin malfunctioning like that, _especially _the FTL engine, you should not be there."

Alyx looked back up at Eli. "Dad, when other systems malfunction, I am allowed to help in their repairs, but when it comes to the FTL engine, I'm not allowed near it when things go wrong. I know it has something to do with what happened in Sector C when I was just a child. What happened in Sector C Dad?"

Eli decided he could not continue shielding the truth from his daughter. He had shielded her from everything, hoping to protect her after his wife had died. "It was terrible what happened in Sector C," Eli said quietly. "It was the reason the FTL project was shut down for so long. We tried to activate a small window into subspace so we could send in a transmitter, to gather data. The core began to destabilize like it did just moments ago.

There was no containment field around the core and there was an explosion. An unstable subspace window was suddenly opened and everyone in the test chamber, including Gordon, were sucked inside. The transmitter went with them and it sent no data. We believed that everyone that had been taken into it had been torn apart, but somehow, Gordon survived and he returned sixteen years after the incident at Black Mesa."

"That is terrible!" Alyx cried. "I understand why you did not tell me about it all this time." Eli nodded and asked Gordon to step outside for a moment. He and Gordon left Alyx behind in her quarters so they could talk.

"Gordon, there is something you must know," Eli said. Gordon raised both of his eyebrows. "What is that?"

Eli paused for a moment before he replied. "It's about what happened before the experiment at Sector C began. Our sponsor who provided us with the instructions and materials to build the first FTL system told me to prepare for unforeseen consequences. I honestly have no idea why I did not express my concerns about him and abort the test." Gordon had never met the sponsor, but something about what Eli told him, caused him to feel a chill go down his spine.


	5. Hostile Space

After Gordon's conversation with Eli, he had gone to his quarters to rest while the repair team repaired the FTL engine. While he was resting, he fell asleep. While asleep, he had a disturbing dream.

In his dream, he was back at Sector C working on the FTL project. Suddenly, the system began to destabilize and the FTL engine systems began to short circuit. "Everyone get out!" Gordon yelled. He watched as people began to run for the blast doors, but suddenly, the FTL core exploded and he saw the unstable subspace window open up.

Gordon watched as fellow colleagues were pulled in, screaming, and he was horrified. It was not long before he also felt himself lift off the ground and he became filled with a feeling of dread as he was pulled inside and then all he saw was darkness.

Soon, a white light appeared in front of him and he watched a man step out of the darkness into the light. The man wore a business suit and a tie, had dark hair, and carried a brief case in one hand. He adjusted his tie with one hand and then he smiled at Gordon. "Mister Freeman. I require your assistance. I am not at liberty to explain why I need your assistance, but just remember this… It is extremely important." Then Gordon sat up, in a bed he did not recognize. The bed was in an apartment he had never been in before. He quickly got out of bed and rushed to a bathroom and he turned on the sink and splashed water on his face. Then he looked into the mirror and saw the face of the man in the business suit in the mirror, looking back at him.

Gordon suddenly sat up, yelled, and then realized that he was in his quarters, aboard the Freeman. However, he was disturbed by his dream, because it mostly consisted of real events, except, he had no idea who the man in the business suit was.

He quickly got out of bed and got into his hazard suit again. He hurried back to FTL Management to see how the repairs were going. When he got there, a member of the repair team noticed him. "Ah, Doctor Freeman! We just figured out the problem and we fixed it! The next time you use the FTL engine, the core will not destabilize. Unfortunately, we still have about seven hours left of repair work to fix the damage to the systems and the engine itself, which was caused by the destabilization."

Gordon nodded. "Good." The repair worker noticed that Gordon seemed distraught. "Mister Freeman, maybe you should report to the infirmary, or maybe report to the ship's psychologist for an analysis."

"No, I do not think that is necessary," Gordon replied. "I am fine." The repair worker nodded and then returned to his work. Gordon quickly hurried out of FTL Management and then left the Systems Control Sector. He went to the bridge and found night shift workers there, keeping watch for any signs of anomalies in space, or for possible alien encounters. They obviously had no idea where they were, because they had left subspace prematurely.

The team noticed Gordon, nodded in acknowledgement and then they looked back at the view screen that showed surveillance footage of the outside of the ship from the sides, the back, and the front. Suddenly, they noticed a subspace window open up behind the Freeman. Seconds later, a ship exited. The ship that came out of subspace was massive. "What the hell?" Gordon just stared at the ship. He estimated that the ship was about the size of the entire Black Mesa facility.

A member of the navigation crew attempted to communicate with the ship, using several different frequencies. "This is the Freeman, please respond." Gordon did not expect the aliens to understand the message; however, there was an audio response. "Your language is a language from a planet called Earth!" Gordon was extremely surprised that the aliens could understand.

"Let me talk to the aliens," Gordon said. "I am Gordon Freeman, the commander of Systems Control. We are not hostile and we did not trespass in your space intentionally. We had a technical problem. I am also curious how you know our language."

The alien replied, "Your language is in our database and every senior officer aboard our ships can understand you. It does not matter if you are hostile. Surrender your ship to us or be destroyed!"

"We will not surrender," Gordon said. "Please, I already explained that we did not trespass here intentionally." There was no response. "Listen, we will leave as soon as our FTL engine is running again. You do not need to attack us."

The only response Gordon received was the sound of an explosion on the ship's hull, as well as a rumbling sound. The explosion caused the whole ship to tremble. Gordon fell to the ground and then quickly got up. "They are firing at us!" said a member of the navigation crew. "Get this ship as far away from these aliens as possible!" Gordon instructed. He quickly turned on the intercom and told the repair crew at FTL Management what was happening. Before they could respond, the aliens fired again and the intercom link was severed.

"Doctor Freeman, their last shot disabled several systems, including the intercom! We have also taken severe damage on the outside of the ship and we need to evacuate Deck four, Sectors B through D immediately!"

An alarm was activated, followed by a recording that said, "All civilians, seek shelter in Deck three, Sector D, immediately!"

"Alright, we've got to fire back at these aliens!" Gordon yelled. The alien ship fired again and this time, the surveillance systems completely went down so the enemy ship was no longer visible. There was also a major hull breach on Deck four in Sector C and anyone that was there would be sucked out into space. The Security team, commanded by Barney Calhoun, rushed into the bridge and took positions while the military defense team hurried to the Combat Center of the ship on Deck two, Sector A.

Two missiles were fired at the enemy ship. Each missile hit the force field that surrounded the alien ship and exploded, causing no damage to the ship. Gordon quickly hurried out of the bridge to go back to Systems Control, hoping to get the force field online. When he got there, the engineering team was already working on the problem.

"Doctor Freeman, the force field isn't coming online!" someone said. "The destabilization of the FTL engine caused damage to other systems in this sector!"

Another shot from the aliens shook the ship, this time Sectors D and C on deck four were completely destroyed. There was nothing left there but a giant hole in the ship's hull. The teams continued working on the force field, rerouting power to the system any way possible.

"Doctor Freeman, I think we've got it!" Just then, the force field surrounded the Freeman and when the aliens fired again, the Freeman was protected. "How long will we be safe?" Gordon asked.

"Their weapons are powerful and our protective force field is down to thirty percent already, from just one shot!" someone cried out. Just then, the intercom came back on, but there was a lot of static. The voice on the intercom was the voice of the alien commander. "Every human on the Freeman, surrender your ship now and we will not destroy you. Refuse and we will show no mercy!"

The alien ship fired again and this time, the protective force field was taken down completely and the systems powering the force field were all short circuited. "This is your last warning, surrender or be destroyed!" said the alien voice on the intercom. About a second later, a member of the repair crew hurried into the room where Gordon was. "Doctor Freeman, the FTL engine is ready, although we were unable to repair all of the systems, so it might be unstable. However, our only options are to die from an unstable FTL drive, or at the hands of aliens!"

"A short jump might be okay," Gordon said. "As long as it's not left on too long, you can continue the repairs after we have left subspace again. Let's move!" They both hurried back to FTL Management and Gordon gave the order. The FTL engine was powered up and then the team prepared to open up a subspace window.

The alien ship fired again as the subspace window opened up and the Freeman entered subspace. Luckily, the alien ship missed their target when the Freeman and the crew escaped.


End file.
